ArticleNucleic acids research2017
AMMOS2: a web server for protein-ligand-water complexes refinement via molecular mechanics.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Novel Drug-like HsrA Inhibitors Exhibit Potent Narrow-Spectrum Antimicrobial Activities againstInternational journal of molecular sciences · 2024Article
- Engineering of a mammalian VMAT2 for cryo-EM analysis results in non-canonical protein folding.Nature communications · 2024Article
- Insight into binding of endogenous neurosteroid ligands to the sigma-1 receptor.Nature communications · 2024Article
- Trends in application of advancing computational approaches in GPCR ligand discovery.Experimental biology and medicine (Maywood, N.J.) · 2021Review
- Virtual screening web servers: designing chemical probes and drug candidates in the cyberspace.Briefings in bioinformatics · 2021Review
- New machine learning and physics-based scoring functions for drug discovery.Scientific reports · 2021Article
- Prioritizing potential ACE2 inhibitors in the COVID-19 pandemic: Insights from a molecular mechanics-assisted structure-based virtual screening experiment.Journal of molecular graphics & modelling · 2020Article
- Machine learning classification can reduce false positives in structure-based virtual screening.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Molecular Structure, Binding Affinity, and Biological Activity in the Epigenome.International journal of molecular sciences · 2020Review
- A Free Web-Based Protocol to Assist Structure-Based Virtual Screening Experiments.International journal of molecular sciences · 2019Article
- Electrostatic mechanism of V600E mutation-induced B-Raf constitutive activation in colorectal cancer: molecular implications for the selectivity difference between type-I and type-II inhibitors.European biophysics journal : EBJ · 2019Article
- DPubChem: a web tool for QSAR modeling and high-throughput virtual screening.Scientific reports · 2018Article
- Identification by Molecular Docking ofHomoisoflavones from Leopoldia comosa as Ligands of Estrogen Receptors.Molecules (Basel, Switzerland) · 2018Article
- Annotation of Peptide Structures Using SMILES and Other Chemical Codes-Practical Solutions.Molecules (Basel, Switzerland) · 2017Review
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8 authors.
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Abstract
AMMOS2 is an interactive web server for efficient computational refinement of protein-small organic molecule complexes. The AMMOS2 protocol employs atomic-level energy minimization of a large number of experimental or modeled protein-ligand complexes. The web server is based on the previously developed standalone software AMMOS (Automatic Molecular Mechanics Optimization for in silico Screening). AMMOS utilizes the physics-based force field AMMP sp4 and performs optimization of protein-ligand interactions at five levels of flexibility of the protein receptor. The new version 2 of AMMOS implemented in the AMMOS2 web server allows the users to include explicit water molecules and individual metal ions in the protein-ligand complexes during minimization. The web server provides comprehensive analysis of computed energies and interactive visualization of refined protein-ligand complexes. The ligands are ranked by the minimized binding energies allowing the users to perform additional analysis for drug discovery or chemical biology projects. The web server has been extensively tested on 21 diverse protein-ligand complexes. AMMOS2 minimization shows consistent improvement over the initial complex structures in terms of minimized protein-ligand binding energies and water positions optimization. The AMMOS2 web server is freely available without any registration requirement at the URL: http://drugmod.rpbs.univ-paris-diderot.fr/ammosHome.php.
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